X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=68b5d288ee18a512320f12b1f41a918bf035cbe2;hb=df81a9e1abd4d4424d6d24b37d93f17bffd3649c;hp=4526eba1eb7e054094dabad5e55bf7c4ba98062f;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 4526eba..68b5d28 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -23,6 +23,7 @@ package jalview.io; import jalview.api.AlignExportSettingI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; import jalview.util.MessageManager; import java.io.BufferedReader; @@ -38,12 +39,22 @@ import java.net.MalformedURLException; import java.net.URL; import java.util.zip.GZIPInputStream; + +import jalview.ws.dbsources.Pfam; +import jalview.ws.dbsources.Rfam; + /** * implements a random access wrapper around a particular datasource, for * passing to identifyFile and AlignFile objects. */ public class FileParse { + protected static final String SPACE = " "; + + protected static final String TAB = "\t"; + + private static final String GZ_EXT = ".gz"; + /** * text specifying source of data. usually filename or url. */ @@ -51,6 +62,7 @@ public class FileParse public File inFile = null; + /** * a viewport associated with the current file operation. May be null. May * move to different object. @@ -94,7 +106,7 @@ public class FileParse */ protected String suffix = null; - protected String type = null; + protected DataSourceType dataSourceType = null; protected BufferedReader dataIn = null; @@ -124,9 +136,8 @@ public class FileParse { if (from == null) { - throw new Error( - MessageManager - .getString("error.implementation_error_null_fileparse")); + throw new Error(MessageManager + .getString("error.implementation_error_null_fileparse")); } if (from == this) { @@ -138,7 +149,7 @@ public class FileParse suffix = from.suffix; errormessage = from.errormessage; // inherit potential error messages error = false; // reset any error condition. - type = from.type; + dataSourceType = from.dataSourceType; dataIn = from.dataIn; if (dataIn != null) { @@ -178,7 +189,7 @@ public class FileParse } if (!error) { - if (fileStr.toLowerCase().endsWith(".gz")) + if (fileStr.toLowerCase().endsWith(GZ_EXT)) { try { @@ -203,16 +214,16 @@ public class FileParse private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception { - BufferedReader inData = new BufferedReader(new InputStreamReader( - new GZIPInputStream(inputStream))); + BufferedReader inData = new BufferedReader( + new InputStreamReader(new GZIPInputStream(inputStream))); inData.mark(2048); inData.read(); inData.reset(); return inData; } - private boolean checkURLSource(String fileStr) throws IOException, - MalformedURLException + private boolean checkURLSource(String fileStr) + throws IOException, MalformedURLException { errormessage = "URL NOT FOUND"; URL url = new URL(fileStr); @@ -220,7 +231,7 @@ public class FileParse // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via // Kenny Sabir Exception e = null; - if (fileStr.toLowerCase().endsWith(".gz")) + if (isGzipped(fileStr)) { try { @@ -241,10 +252,8 @@ public class FileParse { if (e != null) { - throw new IOException( - MessageManager - .getString("exception.failed_to_resolve_gzip_stream"), - e); + throw new IOException(MessageManager + .getString("exception.failed_to_resolve_gzip_stream"), e); } throw q; } @@ -254,6 +263,27 @@ public class FileParse } /** + * Answers true if the filename (or URL) has a format which Jalview recognises + * as denoting gzipped content. + *

+ * Currently this means having a ".gz" extension, or ending in "/gzipped" or + * "?gz=1" (used to retrieve gzipped from Pfam and Rfam respectively). + * + * @param filename + * @return + */ + protected static boolean isGzipped(String filename) + { + if (filename == null) + { + return false; + } + String lower = filename.toLowerCase(); + return lower.endsWith(GZ_EXT) || lower.endsWith(Pfam.GZIPPED) + || lower.endsWith(Rfam.GZIPPED); + } + + /** * sets the suffix string (if any) and returns remainder (if suffix was * detected) * @@ -274,23 +304,47 @@ public class FileParse } /** + * not for general use, creates a fileParse object for an existing reader with + * configurable values for the origin and the type of the source + */ + public FileParse(BufferedReader source, String originString, + DataSourceType sourceType) + { + dataSourceType = sourceType; + error = false; + inFile = null; + dataName = originString; + dataIn = source; + try + { + if (dataIn.markSupported()) + { + dataIn.mark(READAHEAD_LIMIT); + } + } catch (IOException q) + { + + } + } + + /** * Create a datasource for input to Jalview. See AppletFormatAdapter for the * types of sources that are handled. * * @param fileStr * - datasource locator/content - * @param type + * @param sourceType * - protocol of source * @throws MalformedURLException * @throws IOException */ - public FileParse(String fileStr, String type) + public FileParse(String fileStr, DataSourceType sourceType) throws MalformedURLException, IOException { - this.type = type; + this.dataSourceType = sourceType; error = false; - if (type.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { if (checkFileSource(fileStr)) { @@ -301,19 +355,19 @@ public class FileParse { throw new IOException(MessageManager.formatMessage( "exception.problem_opening_file_also_tried", - new String[] { inFile.getName(), suffixLess, - errormessage })); + new String[] + { inFile.getName(), suffixLess, errormessage })); } } else { throw new IOException(MessageManager.formatMessage( - "exception.problem_opening_file", - new String[] { inFile.getName(), errormessage })); + "exception.problem_opening_file", new String[] + { inFile.getName(), errormessage })); } } } - else if (type.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { try { @@ -350,13 +404,13 @@ public class FileParse error = true; } } - else if (type.equals(AppletFormatAdapter.PASTE)) + else if (sourceType == DataSourceType.PASTE) { errormessage = "PASTE INACCESSIBLE!"; dataIn = new BufferedReader(new StringReader(fileStr)); dataName = "Paste"; } - else if (type.equals(AppletFormatAdapter.CLASSLOADER)) + else if (sourceType == DataSourceType.CLASSLOADER) { errormessage = "RESOURCE CANNOT BE LOCATED"; java.io.InputStream is = getClass() @@ -382,15 +436,15 @@ public class FileParse else { errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" - + (type != null ? type : "null") + "'"; + + (sourceType != null ? sourceType : "null") + "'"; error = true; } if (dataIn == null || error) { // pass up the reason why we have no source to read from throw new IOException(MessageManager.formatMessage( - "exception.failed_to_read_data_from_source", - new String[] { errormessage })); + "exception.failed_to_read_data_from_source", new String[] + { errormessage })); } error = false; dataIn.mark(READAHEAD_LIMIT); @@ -421,9 +475,9 @@ public class FileParse { return dataIn.readLine(); } - throw new IOException(MessageManager.formatMessage( - "exception.invalid_source_stream", - new String[] { errormessage })); + throw new IOException(MessageManager + .formatMessage("exception.invalid_source_stream", new String[] + { errormessage })); } /** @@ -457,20 +511,27 @@ public class FileParse } /** - * rewinds the datasource the beginning. + * Rewinds the datasource to the marked point if possible + * + * @param bytesRead * */ - public void reset() throws IOException + public void reset(int bytesRead) throws IOException { + if (bytesRead >= READAHEAD_LIMIT) + { + System.err.println(String.format( + "File reset error: read %d bytes but reset limit is %d", + bytesRead, READAHEAD_LIMIT)); + } if (dataIn != null && !error) { dataIn.reset(); } else { - throw new IOException( - MessageManager - .getString("error.implementation_error_reset_called_for_invalid_source")); + throw new IOException(MessageManager.getString( + "error.implementation_error_reset_called_for_invalid_source")); } } @@ -581,4 +642,20 @@ public class FileParse } // could also set export/import settings } + + /** + * Returns the preferred feature colour configuration if there is one, else + * null + * + * @return + */ + public FeatureSettingsModelI getFeatureColourScheme() + { + return null; + } + + public DataSourceType getDataSourceType() + { + return dataSourceType; + } }